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| baseCallMetrics | Gather basecalling metrics from a Run (using Run's ConversionStats.xml file). |
| basecallQC | The basecallQC object and constructor. |
| basecallQC-basecallQC | The basecallQC object and constructor. |
| basecallQC-class | The basecallQC object and constructor. |
| BCL2FastQparams | The Parameters for BCL2FastQparams object. |
| BCL2FastQparams-BCL2FastQparams | The Parameters for BCL2FastQparams object. |
| BCL2FastQparams-class | The Parameters for BCL2FastQparams object. |
| createBasemasks | Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7). |
| createBCLcommand | Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7. |
| demultiplexMetrics | Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file). |
| demuxBarplot | Barplot of Illumina demultiplexing statistics. |
| demuxBarplot-method | Barplot of Illumina demultiplexing statistics. |
| demuxBarplot.basecallQC | Barplot of Illumina demultiplexing statistics. |
| demuxBoxplot | Boxplot of Illumina demultiplexing statistics. |
| demuxBoxplot-method | Boxplot of Illumina demultiplexing statistics. |
| demuxBoxplot.basecallQC | Boxplot of Illumina demultiplexing statistics. |
| indexlengths | Index lengths |
| indexlengths,BCL2FastQparams-method, | Index lengths |
| indexlengths-method | Index lengths |
| indexlengths.bcl2fastqparams | Index lengths |
| interOpsReport | Function to parse InterOps files and generate summary reports |
| makeFQTable | Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead |
| passFilterBar | Barplot of Illumina basecalling statistics for reads passing filter. |
| passFilterBar-method | Barplot of Illumina basecalling statistics for reads passing filter. |
| passFilterBar.basecallQC | Barplot of Illumina basecalling statistics for reads passing filter. |
| passFilterBoxplot | Boxplot of Illumina basecalling statistics for reads passing filter. |
| passFilterBoxplot-method | Boxplot of Illumina basecalling statistics for reads passing filter. |
| passFilterBoxplot.basecallQC | Boxplot of Illumina basecalling statistics for reads passing filter. |
| passFilterTilePlot | Tile plot of Illumina basecalling statistics for reads passing filter. |
| passFilterTilePlot-method | Tile plot of Illumina basecalling statistics for reads passing filter. |
| passFilterTilePlot.basecallQC | Tile plot of Illumina basecalling statistics for reads passing filter. |
| readlengths | Read lengths |
| readlengths,BCL2FastQparams-method, | Read lengths |
| readlengths-method | Read lengths |
| readlengths.bcl2fastqparams | Read lengths |
| reportBCL | Generate basecallQC report |
| reportBCL-method | Generate basecallQC report |
| reportBCL.basecallQC | Generate basecallQC report |
| summaryConvStatsTable | Creates an HTML table of per sample summary statistics from basecalling results |
| summaryConvStatsTable-method | Creates an HTML table of per sample summary statistics from basecalling results |
| summaryConvStatsTable.basecallQC | Creates an HTML table of per sample summary statistics from basecalling results |
| summaryDemuxTable | Generate an HTML table of per sample summary demultiplexing statistics |
| summaryDemuxTable-method | Generate an HTML table of per sample summary demultiplexing statistics |
| summaryDemuxTable.basecallQC | Generate an HTML table of per sample summary demultiplexing statistics |
| validateBCLSheet | Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7 |